Duplicate backup in Server and FTP Repository

[jgpcandrepair]

I have a server backup set up to run every night and be put into an FTP repository. On several occasions (random, no pattern noticed) the backup appears in the FTP repository as well as the server repository. The problem with this is that the backups in the server repository are counting towards the space usage for the domains. In short, how do I ensure duplicate backups are not placed in the server repository? Thanks!